Grain size and lodging resistance determine rice yield by affecting grain weight, and are also associated with secondary cell wall (SCW) thickness. In this study, we demonstrate the dual roles of OsCesAs, which encode cellulose synthases, in the regulation of grain size and culm mechanical strength through the brassinosteroid (BR) signaling pathway. RT-qPCR analysis revealed that the transcript levels of all rice CesA gene family members were induced by exogenous brassinolide (BL) treatment. Moreover, OsCesA4/7/9, which are involved in secondary cell wall synthesis, exhibited similar expression patterns during rice culm and grain development. Overexpression of OsCesA4/9 not only enhanced secondary cell wall thickness and cellulose content in culms, thereby improving mechanical strength, but also increased grain size. OsBZR1 directly binds to the promoters of OsCesA4/7/9 through a regulatory mechanism distinct from that in Arabidopsis, thus negatively regulating their expression. This ultimately results in increased culm cellulose content and mechanical strength in the cr-osbzr1 mutant. However, analysis of culm mechanical strength and grain size in mutants of qGL3, OsGSK3, and OsBZR1, which are key components of the BR signaling pathway, revealed a weak correlation between these two traits. This work helps breeders better understand the important functions of BR signaling in plant growth and development, enabling targeted molecular design breeding of rice for lodging tolerance and grain size.

Brassinosteroid (BR) signaling plays a critical role in rice (Oryza sativa L.) grain development. GLYCOGEN SYNTHASE KINASE 3 (OsGSK3), a negative regulator of BR signaling, suppresses the transcriptional activity of OsBZR1 through phosphorylation. In this study, we employed a phosphoproteomic approach to construct an OsGSK3-mediated regulatory network. Within this network, we identified FLOWERING CONTROL LOCUS A (OsFCA) as a positive regulator of BR signaling and grain length, with m-Osfca mutants exhibiting significantly lower sensitivity to brassinolide treatment. Importantly, OsGSK3 interacts with and phosphorylates OsFCA on serine residues S43 and S45, and then forms condensates via liquid-liquid phase separation. Phosphorylated OsFCA promotes the translocation of the OsGSK3-OsFCA complex into the cytoplasm. Within the cytoplasm, OsGSK3 and OsFCA no longer exist in a condensate state. This mechanism provides precise regulation of grain length in rice. Notably, Osfca mutants are late-flowering, with OsFCA promoting heading under long-day conditions by repressing the expression of Grain number, plant height and heading date 7 (Ghd7) while activating that of Early heading date 1 (Ehd1), Heading date 3a (Hd3a), and RICE FLOWERING LOCUS T 1 (RFT1), which is potentially modulated by OsGSK3. This study clarifies the BR signaling transduction network by identifying OsFCA as a positive BR signaling component that regulates grain development and heading date, providing theoretical foundations for molecular breeding design in rice.

RISBZ1 encodes the transcription factor bZIP58, which regulates grain filling; intron editing of RISBZ1 to eliminate aberrant alternatively spliced transcripts increased grain weight without compromising key agronomic traits under normal conditions, and enhanced grain weight and quality under heat stress conditions.

Rice microRNA1439 (miR1439) belongs to a conserved miRNA family and its expression is induced by various biotic and abiotic stresses. However, whether and how miR1439 is involved in disease resistance in rice is unclear. In this study, we found that the expression of miR1439 was significantly up-regulated upon Magnaporthe oryzae infection. Overexpressing miR1439 leads an enhanced disease resistance against M. oryzae, whereas blocking the function of miR1439 by overexpressing a target mimic resulted in increased disease susceptibility. Further investigation revealed that miR1439 directly targets and represses the expression of RING-H2 finger protein with potential E3 ligase activity (OsRFPH2-6), a negative regulator of disease resistance. Interestingly, transgenic lines blocking miR1439 exhibited increased grain length and grain weight, while overexpressing miR1439 leads to decreased grain length and grain weight, possibly due to the repression of FLOURY ENDOSPERM2 (OsFLO2), a target gene of miR1439. Thus, our findings highlight the pivotal role of miR1439 in mediating disease resistance and grain development in rice, and provide a potential target for breeding resistant cultivars without yield penalty.

Urban flooding presents a significant challenge in Chinese cities, necessitating a deeper understanding of the coupling effects of China's urban flood resilience for effective resilience planning. This study introduces a four-component Environment-Institution-Infrastructure-Agent (EIFA) framework and utilizes an updated correlation network approach to analyze the temporal variation of coupling effects of urban flood resilience across 639 Chinese cities from 2012 to 2022. The findings indicate a decline in synergy and increased tradeoffs, primarily due to intensified competition within and between institutional and infrastructural sectors, marginal impacts of infrastructure investments, and socially excessive infrastructure. The study also highlights the agent component's strong internal and inter-component coupling effects, implying the effectiveness of China's people-centered resilience strategies, though risks of decoupling remain. Additionally, it notes a good match between societal urban flood resilience and natural flood risks, while natural vegetation loss due to urban expansion is noteworthy. The study further suggests that refining agent-focused deposit and insurance policies could coordinatively enhance urban flood resilience, as these elements are hubs within the network. The updated network-based framework and its findings offer insights for informing and optimizing urban flood resilience planning in China.

A soybean TF-target prediction tool based on gene co-expression and machine learning.

Previous studies have identified oxidative stress and inflammatory responses in granulosa cells (GCs) of periparturient dairy cows. However, whether non-esterified fatty acids (NEFA)-induced endoplasmic reticulum (ER) stress is involved in GC apoptosis remains unclear. In this study, treatment with NEFA (0.9 mM, 24 h) activated the ER stress pathway. This was evidenced by increased expression of both CHOP and GRP78. Furthermore, upregulation of pro-apoptotic factors BAX and Caspase-3 and downregulation of the anti-apoptotic factor Bcl-2 were observed. Pretreatment of GCs with 4-phenylbutyric acid (4-PBA, 2.5 mM, 2 h) reversed the ER stress and apoptotic effects. This suggests that NEFA-induced apoptosis is mediated through activation of the PERK pathway of ER stress, and that 4-PBA alleviates this effect. Furthermore, targeted metabolomics revealed disruptions in lipid and hormone metabolism in GCs following NEFA treatment. Analysis revealed an increase in the levels of 26 types of fatty acids, while a decrease was detected in the levels of 3 types of fatty acids. In summary, NEFA induces ER stress and disrupts intracellular fatty acid, ultimately leading to cell apoptosis. Our findings offer valuable insights for developing strategies to regulate follicular development in dairy cows and mitigate the impacts of postpartum negative energy balance (NEB).

Rice grain yield is primarily determined by three key agronomic traits: panicle number, grain number per panicle, and grain weight(GW). However, the inherent tradeoffs among these yield components remain a persistent challenge in rice breeding programs. Notably, compared with GW, brown rice weight(BRW) provides a more direct metric associated with actual grain yield potential. In this study, we conducted a two-year replicated genome-wide association study to elucidate the genetic architecture of BRW and identify new loci regulating GW. Among seven consistently detected loci across experimental replicates, four were not co-localized with previously reported genes associated with BRW or GW traits. BRW1.1, one of the four newly identified loci, was found to encode a novel RNA-binding protein. Functional characterization revealed that BRW1.1 acts as a negative regulator of BRW, potentially through modulating m RNA translation processes. Intriguingly, through integrated analysis of mutant phenotypes and haplotype variations, we demonstrated that BRW1.1 mediates the physiological tradeoff between GW and panicle number. This study not only delineates the genetic determinants of BRW but also identifies BRW1.1 as a promising molecular target for breaking the yield component tradeoff in precision rice breeding.

Plant immune receptors and their natural variations play a central role in combating disease-causing pathogens. These immune receptors include intracellular nucleotide-binding leucine-rich repeat (LRR) receptors (NLRs) and cell-surface pattern recognition receptors (PRRs) that can be further classified as receptor-like proteins (RLPs) and receptor-like kinases (RLKs). Although the NLRome has been characterized, the repertoire and extent of diversity of PRRome remain undetermined in rice. In this study, we examined the diversity of immune receptor genes using high-quality genomes of 309 rice accessions from 8 species within the genus Oryza. A total of 376 310 immune receptor genes were identified, including 149 592 NLR-coding genes and 226 718 PRR coding genes. Shannon entropy analysis revealed a set of immune receptors that display significant intra-species and inter-species diversity in rice. In general, RLPs are more variable than RLKs, while NLRs and LRR-RLPs are more variable than LRR-RLKs. Additionally, NLR and PRR genes exhibit contrasting shoot/root expression patterns, with NLRs generally skewed towards root expression. Furthermore, we found that the size of the LRR-RLK gene families correlates with local annual precipitation, suggesting a stronger selection pressure on LRR-RLK genes in rice accessions grown under wet conditions than dry conditions. In sum, this pan-genomic analysis not only reveals the extensive diversity of the immune receptor repertoires in rice but also provides potential target genes for improving disease resistance in rice.

Seed germination is a key process in the life cycle of seed plants. The initiation of seed germination requires the activity of specific internal signaling molecules, such as hormones and reactive oxygen species (ROS), and is dependent on external environmental factors, such as water, temperature, and light. Seed germination is a complex trait that is regulated by multiple factors, including transcript, protein, and metabolite levels. This review highlights current knowledge relating to the regulatory roles of hormones, ROS, small RNAs, epigenetic modifications, post-translational modifications, and environmental cues on seed germination, mainly focusing on Arabidopsis and rice. The review on the molecular regulation of seed germination contributes to the improvement of crop seed quality using bio-breeding approaches.

Lodging causes a reduction in wheat (Triticum aestivum L.) yield and quality. A shorter plant height (PH) can reduce the incidence of lodging. The overuse of nitrogen promotes excessive vegetative growth, leads to taller plants, and increases lodging risk. Here, we utilized genome-wide association studies (GWASs) to explore the genetic basis of PH and the nitrogen effect index (NEI), a parameter to estimate the responses of PH under varying nitrogen conditions, using 21,201 SNP markers from the Illumina Wheat 90K SNP array. A total of 191 wheat varieties from Yellow and Huai Valley regions of China, as well as other global regions, were analyzed across two growing seasons under four nitrogen treatments, namely N0 (0 kg/ha), N150 (150 kg/ha), N210 (210 kg/ha), and N270 (270 kg/ha). GWAS results showed that 30 genetic markers were associated with PH, explaining phenotypic variance from 5.92% to 13.69%. Additionally, nine significant loci were associated with the NEI. Notably, markers on chromosomes 1A and 6B were linked to both PH and the NEI, which were insensitive to low- and high-nitrogen fertilizers. In addition, the PH of the three cultivars (Zhoumai16, Zhoumai13, and Bima1) showed little variation in four nitrogen fertilizer levels. This study identified key genetic markers associated with wheat PH and the NEI, providing insights for optimizing nitrogen use in wheat breeding.

Gibberellins (GAs) play crucial roles in regulating plant architecture and grain yield of crops. In rice, the inactivation of endogenous bioactive GAs and their precursors by GA 2-oxidases (GA2oxs) regulates stem elongation and reproductive development. However, the regulatory mechanisms of GA2ox gene expression, especially in rice reproductive organs, are unknown. The BEL1-like homeodomain protein OsBLH4, a negative regulatory factor for the rice OsGA2ox1 gene, was identified in this study. Loss of OsBLH4 function results in decreased bioactive GA levels and pleiotropic phenotypes, including reduced plant height, decreased grain number per panicle, and delayed heading date, as also observed in OsGA2ox1-overexpressing plants. Consistent with the mutant phenotype, OsBLH4 was predominantly expressed in shoots and young spikelets; its encoded protein was exclusively localized in the nucleus. Molecular analysis demonstrated that OsBLH4 directly bound to the promoter region of OsGA2ox1 to repress its expression. Genetic assays revealed that OsBLH4 acts upstream of OsGA2ox1 to control rice plant height, grain number, and heading date. Taken together, these results indicate a crucial role for OsBLH4 in regulating rice plant architecture and yield potential via regulation of bioactive GA levels, and provide a potential strategy for genetic improvements of rice.

Brassinosteroids (BRs) are a class of phytohormones that regulate plant growth and development. In previous studies, we cloned and identified PROTEIN PHOSPHATASE WITH KELCH-LIKE1 (OsPPKL1) as the causal gene for the quantitative trait locus GRAIN LENGTH3 (qGL3) in rice (Oryza sativa). We also showed that qGL3/OsPPKL1 is mainly located in the cytoplasm and nucleus and negatively regulates BR signaling and grain length. Because qGL3 is a negative regulator of BR signaling, its turnover is critical for rapid response to changes in BRs. Here, we demonstrate that qGL3 interacts with the WD40-domain-containing protein WD40-REPEAT PROTEIN48 (OsWDR48), which contains a nuclear export signal (NES). The NES signal is crucial for the cytosolic localization of OsWDR48 and also functions in the self-turnover of qGL3. We show that OsWDR48 physically interacts with and genetically acts through qGL3 to modulate BR signaling. Moreover, qGL3 may indirectly promote the phosphorylation of OsWDR48 at the Ser-379 and Ser-386 sites. Substitutions of both phosphorylation sites in OsWDR48 to non-phosphorylatable alanine enhanced the strength of the OsWDR48-qGL3 interaction. Furthermore, we found that brassinolide can promote the accumulation of non-phosphorylated OsWDR48, leading to strong interaction intensity between qGL3 and OsWDR48. Taken together, our results show that OsWDR48 facilitates qGL3 retention and induces degradation of qGL3 in the cytoplasm. These findings suggest that qGL3 self-modulates its turnover by binding to OsWDR48 to regulate its cytoplasmic localization and stability, leading to efficient orchestration of BR signal transduction in rice.

Amino acid transporters (AATs) have been shown to be involved in immune responses during plant-pathogen interactions; however, the molecular mechanism by which they function in this process remains unclear. Here, we used a joint analysis of a genome-wide association study and quantitative trait locus (QTL) mapping to identify MEMBRANE PROTEIN 1, which acts as a QTL in rice against blast fungus. Heterogeneous expression of OsMP1 in yeast supported its function in transporting a wide range of amino acids, including Thr, Ser, Phe, His, and Glu. OsMP1 could also mediate 15N-Glu efflux and influx in Xenopus oocyte cells. The expression of OsMP1 was significantly induced by Magnaporthe oryzae in the resistant rice landrace Heikezijing, whereas no such induction was observed in the susceptible landrace Suyunuo. Overexpressing OsMP1 in Suyunuo enhanced disease resistance to blast fungus and leaf blight bacterium without resulting in a yield penalty. In addition, the overexpression of OsMP1 led to increased accumulation of Thr, Ser, Phe, and His in the leaves and this contributed to the reduced disease susceptibility, which was associated with up-regulation of the jasmonic acid pathway. Our results demonstrate the important role of OsMP1 in disease resistance in rice and provide a potential target for breeding more resistant cultivars without reducing yield.

Rice blast is one of the most devastating diseases, causing a significant reduction in global rice production. Developing and utilizing resistant varieties has proven to be the most efficient and cost-effective approach to control blasts. However, due to environmental pressure and intense pathogenic selection, resistance has rapidly broken down, and more durable resistance genes are being discovered. In this paper, a novel wall-associated kinase (WAK) gene, Pb4, which confers resistance to rice blast, was identified through a genome-wide association study (GWAS) utilizing 249 rice accessions. Pb4 comprises an N-terminal signal peptide, extracellular GUB domain, EGF domain, EGF-Ca2+ domain, and intracellular Ser/Thr protein kinase domain. The extracellular domain (GUB domain, EGF domain, and EGF-Ca2+ domain) of Pb4 can interact with the extracellular domain of CEBiP. Additionally, its expression is induced by chitin and polygalacturonic acid. Furthermore, transgenic plants overexpressing Pb4 enhance resistance to rice blast. In summary, this study identified a novel rice blast-resistant gene, Pb4, and provides a theoretical basis for understanding the role of WAKs in mediating rice resistance against rice blast disease.

Soil salinization is becoming a great threat that reduces crop productivity worldwide. In this study, we found that rice allantoate amidohydrolase (OsAAH) expression was significantly upregulated by salt stress, and its overexpression conferred salt tolerance at the seedling stage. Compared to wild type (WT), the contents of ureides (allantoin and allantoate) were significantly increased in Osaah mutants and reduced in OsAAH overexpression lines both before and after salt treatments. Exogenous allantoin significantly promoted salt tolerance in OsAAH overexpression, but not in Osaah mutants. Subcellular localization showed that OsAAH was also localized to the peroxisomes in addition to the previously reported endoplasmic reticulum (ER). The differential expression of peroxisome-related genes was identified between Osaah mutants and WT. Furthermore, the contents of H2O2 and malondialdehyde (MDA) were significantly accumulated in Osaah mutants and reduced in OsAAH overexpression lines. The activities of antioxidant enzymes were significantly reduced in Osaah mutants and enhanced in OsAAH overexpression under NaCl treatment. The transcription factor OsABI5 could directly bind to OsAAH promoter and activate OsAAH expression. Our findings reveal that OsAAH could be induced by salt stress through the activation of OsABI5 and then confer salt tolerance by enhancing the scavenging capacity of reactive oxygen species (ROS), which contributes to rice breeding in salt tolerance.

Preharvest sprouting (PHS) is an undesirable trait that decreases yield and quality in rice production. Understanding the genes and regulatory mechanisms underlying PHS is of great significance for breeding PHS-resistant rice. In this study, we identified a mutant, preharvest sprouting 39 (phs39), that exhibited an obvious PHS phenotype in the field. MutMap+ analysis and transgenic experiments demonstrated that OsAAH, which encodes allantoate amidohydrolase, is the causal gene of phs39 and is essential for PHS resistance. OsAAH was highly expressed in roots and leaves at the heading stage and gradually increased and then weakly declined in the seed developmental stage. OsAAH protein was localized to the endoplasmic reticulum, with a function of hydrolyzing allantoate in vitro. Disruption of OsAAH increased the levels of ureides (allantoate and allantoin) and activated the tricarboxylic acid (TCA) cycle, and thus increased energy levels in developing seeds. Additionally, the disruption of OsAAH significantly increased asparagine, arginine, and lysine levels, decreased tryptophan levels, and decreased levels of indole-3-acetic acid (IAA) and abscisic acid (ABA). Our findings revealed that the OsAAH of ureide catabolism is involved in the regulation of rice PHS via energy and hormone metabolisms, which will help to facilitate the breeding of rice PHS-resistant varieties.

Soil salinity has a major impact on rice seed germination, severely limiting rice production. Herein, a rice germination defective mutant under salt stress (gdss) was identified by using chemical mutagenesis. The GDSS gene was detected via MutMap and shown to encode potassium transporter OsHAK9. Phenotypic analysis of complementation and mutant lines demonstrated that OsHAK9 was an essential regulator responsible for seed germination under salt stress. OsHAK9 is highly expressed in germinating seed embryos. Ion contents and non-invasive micro-test technology results showed that OsHAK9 restricted K+ efflux in salt-exposed germinating seeds for the balance of K+/Na+. Disruption of OsHAK9 significantly reduced gibberellin 4 (GA4) levels, and the germination defective phenotype of oshak9a was partly rescued by exogenous GA3 treatment under salt stress. RNA sequencing (RNA-seq) and real-time quantitative polymerase chain reaction analysis demonstrated that the disruption of OsHAK9 improved the GA-deactivated gene OsGA2ox7 expression in germinating seeds under salt stress, and the expression of OsGA2ox7 was significantly inhibited by salt stress. Null mutants of OsGA2ox7 created using clustered, regularly interspaced, short palindromic repeat (CRISPR)/CRISPR-associated nuclease 9 approach displayed a dramatically increased seed germination ability under salt stress. Overall, our results highlight that OsHAK9 regulates seed germination performance under salt stress involving preventing GA degradation by mediating OsGA2ox7, which provides a novel clue about the relationship between GA and OsHAKs in rice.

Accumulating experimental data have shown that endogenous hormones play important roles in regulating seed dormancy and germination. Zanthoxylum nitidum is a medicinal plant that propagates via seeds, which require a long dormancy period for normal germination, and complex changes in metabolites occur during the germination process. However, the regulatory network of endogenous hormones and metabolites during the germination of Z. nitidum seeds remains unclear. This study investigated the dynamic changes in the levels of metabolites and endogenous hormones during the germination of Z. nitidum seeds. The results revealed an increase in the levels of gibberellin 3 (GA3), 12-oxophytodienoic acid (OPDA), 1-aminocyclopropane-1-carboxylic acid (ACC) and trans-zeatin (TZ) and decrease in the levels of abscisic acid (ABA), jasmonic acid (JA), N-[(-)-jasmonoyl]-(S)-isoleucine (JA-Ile) and trans-zeatin riboside (TZR). Overall, 112 differential metabolites (DAMs) were screened from 3 seed samples (Sa, Sb and Sc), most of which are related to primary metabolism. A total of 16 DAMs (including 3 monosaccharides, 3 phosphate lipids, 3 carboxylic acids, 1 amino acid, 2 pyrimidines, and 4 nucleotides) were identified in the three sample comparison pairs (Sa vs Sb, Sa vs Sc, and Sb vs Sc); these DAMs were significantly enriched in purine metabolism; glycerophospholipid metabolism, citrate cycle (TCA cycle), alanine, aspartate and glutamate metabolism and pyruvate metabolism. OPDA, ACC and GAs were significantly positively correlated with upregulated metabolites, whereas ABA and JA were significantly positively correlated with downregulated metabolites. Finally, a hypothetical metabolic network of endogenous hormones that regulate seed germination was constructed. This study deepens our understanding of the importance of endogenous hormonal profiles that mediate seed germination.

Many genetic loci for wheat plant height (PH) have been reported, and 26 dwarfing genes have been catalogued. To identify major and stable genetic loci for PH, here we thoroughly summarized these functionally or genetic verified dwarfing loci from QTL linkage analysis and genome-wide association study published from 2003 to 2022. A total of 332 QTL, 270 GWAS loci and 83 genes for PH were integrated onto chromosomes according to their locations in the IWGSC RefSeq v2.1 and 65 QTL-rich clusters (QRC) were defined. Candidate genes in each QRC were predicted based on IWGSC Annotation v2.1 and the information on functional validation of homologous genes in other species. A total of 38 candidate genes were predicted for 65 QRC including three GA2ox genes in QRC-4B-IV, QRC-5A-VIII and QRC-6A-II (Rht24) as well as GA 20-oxidase 2 (TaSD1-3A) in QRC-3A-IV. These outcomes lay concrete foundations for map-based cloning of wheat dwarfing genes and application in breeding.